build.yml

name: build

on:
  pull_request:
    branches:
      - main
  workflow_dispatch:
  push:
    branches:
      - 'main'
      - 'test-build'
    tags:
      - "*"

env:
  PARTICIPANT_DATA:

jobs:
  build:
    name: Build site
    runs-on: ubuntu-latest
    timeout-minutes: 60
    permissions:
      contents: write
    defaults:
      run:
        shell: bash -l {0}
    steps:
      - name: Cancel Previous Runs
        if: ${{ !env.ACT }}
        uses: styfle/cancel-workflow-action@0.11.0
        with:
          access_token: ${{ github.token }}

      - name: Checkout repository
        uses: actions/checkout@v4

      - name: Install micromamba
        uses: mamba-org/setup-micromamba@v1
        with:
          micromamba-version: "1.3.1-0"
          environment-file: conda-linux-64.lock
          environment-name: pgip
          init-shell: bash
          cache-environment: true

      - name: Install pgip dependencies
        run: |
          python -m ipykernel install --user --name pgip --display-name "Population Genomics in Practice (Python)"
          python -m pip install git+https://github.com/NBISweden/pgip-tools
          python -m pip install git+https://github.com/ksamuk/pixy.git

      - name: Install dotenv
        run: |
          R -e "install.packages('dotenv', repos=c(CRAN = 'https://cran.rstudio.com/'))"

      - name: Install TeXLive
        run: |
          sudo apt-get update
          sudo apt-get install texlive texlive-latex-extra

      - name: Install local pgip R package
        run: |
          R -e "library(devtools); devtools::install_local('src/R/pgip', upgrade=F)"

      - name: Setup Quarto
        uses: quarto-dev/quarto-actions/setup@v2
        with:
          version: 1.3.450

      - run: |
          quarto --version

      - name: Add miniconda path
        run: |
          echo "$(dirname $(which R))" >> $GITHUB_PATH
          quarto check

      - name: "Set environment variables"
        run: |
          echo "TEXINPUTS=$TEXINPUTS:$GITHUB_WORKSPACE/src/latex" >> $GITHUB_ENV

      - name: Install dvisvgm
        run: |
          sudo apt-get install dvisvgm

      - name: Render project without publishing
        uses: quarto-dev/quarto-actions/render@v2
        if: ${{ github.event_name == 'pull_request' }}
        with:
          path: docs

      - name: Publish to GitHub Pages
        uses: quarto-dev/quarto-actions/publish@v2
        if: ${{ github.ref_name == 'main' || github.ref_name == 'test-build' }}
        with:
          target: gh-pages
          path: docs
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

      - name: Checkout archived course versions
        env:
          GITHUB_EMAIL: do_not_email@example.com
          GITHUB_USERNAME: gh_action
          TARGET: gh_pages
        run: |
          # Add git info
          git config --global user.email "${{ env.GITHUB_EMAIL }}"
          git config --global user.name "${{ env.GITHUB_USERNAME }}"
          git checkout ${{ env.TARGET }}
          mkdir -p archive
          cd archive

          # Add archive index page
          cat .header.html > index.html

          # Loop tags that match v\d+
          for tag in $(git tag --list v[0-9][0-9][0-9][0-9]); do
              git clone --depth 1 $tag
              contents=$(git tag -n 100 $tag --format "%(contents)")
              echo "<section id=\"$tag\" class=\"level3\">" >> index.html
              echo "<h3 class=\"anchored\" data-anchor-id=\"$tag\">" >> index.html
              echo "<a href=\"$link\">$tag</a>" >> index.html
              echo "</h3>" >> index.html
              echo "<p>$contents</p>" >> index.html
              echo "</section>" >> index.html
          done

          cat .footer.html >> index.html